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Dr. Jennifer Paige brings her sister Lisa to the resort town of Snowfield, Colorado, a small ski resort village nestled in the Rocky Mountains where Jenny works as a doctor. Once in town, the sisters find no one around but a few corpses. At first, their suspicions are that of a serial killer loose in town. After finding the severed heads of the town baker and his wife in an oven, the sisters are found by Sheriff Bryce Hammond, a former FBI agent haunted by the death of a boy he accidentally killed, and his deputies Stu Wargle and Steve Shanning who came to investigate the strange killings.

When they arrive at a nearby hotel, the group finds the writing of a victim on the mirror reading Timothy Flyte. Moments later, Shanning investigates a sound outside with the others finding only his gun, hat and shoes while the rest of him is gone. Returning to the sheriff's office to request aid and create roadblocks around Snowfield, with Wargle revealed to be paranoid and immoral, the group gets a strange call before they are attacked by a strange moth-like creature that rips Wargle's face off prior to Bryce killing it. After implying the creature could be the Devil as it went after him first, Lisa later encounters Wargle while in the bathroom before she and others find his body missing from the morgue.

At that time, Bryce's FBI associates find Flyte, an English academic who theorized the Ancient Enemy, an entity he generalizes as "chaos in the flesh" that periodically wiped out civilizations including that of the Mayas and the Roanoke Island colonists. Joined by an Army commando unit to Snowfield with the Paige sisters and Bryce meeting with him, Flyte accompanies a third of the commando group to investigate with him the only survivor of an attack by a creature in the form of a dog that converted the others in his group.

With the other unit members systematically wiped out by it, the last member giving them a sample he vomited before turning into a puddle of black liquid, Flyte and the group learn the nature of the Ancient Enemy as it sent its converted drones, the Phantoms, to kill off the National Guard stations around the town.

Revealed to actually be an Earth-based amoebic life form that mimics its absorbed victims while gaining their knowledge, the Enemy creates Phantoms as temporary detachments for it to act through before absorbing them back into it. Furthermore, due to its victims' thoughts about it, the Enemy has ultimately perceived itself as a god and had arranged everything so Flyte can assist the creature in revealing its existence to the world. Flyte also learns that the creature's body is physiologically almost identical to crude oil, and could be killed by bacteria bio-engineered to ingest fossil fuels.

However, other than the limited amount they have, the issue remains to get the bacteria into the nucleus that is within the main body of the Enemy. But because the Ancient Enemy is extremely proud, the group has Flyte call it all in its entirety as he played on its god complex by revealing their plan up front. After its nucleus absorbs all the Phantoms while emerging from the sewers to assume a Mother Mass form, Bryce and the Paige sisters fire the bacteria into the Ancient Enemy before it retreats underground with Bryce in pursuit.

While the Paige sisters find themselves dealing with the Phantom in Wargle's image before Jenny seemingly kills it with a gun containing the bacteria, Bryce finds the Ancient Enemy as it assumed the form of the boy he accidentally killed during an FBI drug raid. When the boy grabbed the last vial he had, Bryce shoots at it to expose the creature to its contents as it dies from the bacteria.

Though Bryce reassures Lisa and Jenny that it is gone, with the former stating the townsfolk are at peace, Flyte admits the Ancient Enemy did achieve its victory as he decides to tell the world what happened with a book based on what occurred in Snowfield. Some time later, watching Flyte being interviewed about his book, "The Ancient Enemy", two bar patrons argue about the existence of alien life. Hearing laughter nearby, the patrons turn to see Wargle as he asks them if they want to see something interesting.

Phantoms received largely negative reviews from critics, and currently holds a 13% rating on Rotten Tomatoes, based on 30 reviews.[2]Roger Ebert gave the film 1 star out of 4, saying "If only we could learn to think more kindly of those who digest us, this movie could have ended happily."[3] The film was a flop at the box office, earning $5.6 million in ticket sales.